The strategy of decreasing size with increasing temperature known as Bergmann’s rule operates at geographic scale and in spite of extensive studies still presents a puzzle to researches. The aim of this work was to verify whether patterns of diapausing egg hatching of closely related species are consistent with the expectations from Bergmann’s rule. In a laboratory study of the cryptic species complex of the rotifer Brachionus plicatilis, the response to temperature (17.5, 22.5, and 25.0 °C) of diapausing eggs collected in a pond where the three tested species coexist was assessed by (1) the number of hatchlings emerging or (2) the time needed to hatch. Our results show that the response to temperature from the sediment egg bank is species-dependent. In line with Bergmann’s rule, an association was observed between the hatching response to temperature and organism size. The biggest species increased its proportion in the hatchlings as temperature decreased, and vice versa. The intermediate size species showed an intermediate pattern. Nevertheless, temperature showed a general positive effect on hatching success. Time needed to hatch suggests a signature of Bergmann’s rule, but other factors seem to be affecting this parameter. This is the first study to demonstrate differences in the thermal dependence of diapausing egg hatching among closely related species with different body sizes, and it supports that Bergmann’s rule can be applied to diapause, an important phase in many invertebrate lifecycles.